# HG changeset patch
# User iuc
# Date 1432745675 14400
# Node ID 2cd7e321d259e430118a4a40b81b78a983a2ac71
# Parent  457b09031d57545dec5ff3963c6396810f3523cb
Uploaded

diff -r 457b09031d57 -r 2cd7e321d259 macros.xml
--- a/macros.xml	Tue May 19 07:05:36 2015 -0400
+++ b/macros.xml	Wed May 27 12:54:35 2015 -0400
@@ -89,10 +89,6 @@
         </param>
     </xml>
 
-    <xml name="choose_column">
-        <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
-    </xml>
-
     <token name="@C_AND_O_ARGUMENT@">
         #set $col = list()
         #set $op = list()
@@ -108,7 +104,7 @@
 
     <xml name="c_and_o_argument">
         <repeat name="c_and_o_argument_repeat" title="Applying operations to columns from merged intervals" min="0">
-            <expand macro="choose_column" />
+            <yield />
             <expand macro="choose_operations">
                 <expand macro="math_options" />
                 <expand macro="additional_math_options" />
diff -r 457b09031d57 -r 2cd7e321d259 mapBed.xml
--- a/mapBed.xml	Tue May 19 07:05:36 2015 -0400
+++ b/mapBed.xml	Wed May 27 12:54:35 2015 -0400
@@ -30,7 +30,9 @@
             label="Require reciprocal overlap"
             help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval. (-r)" />
         <expand macro="strand2" />
-        <expand macro="c_and_o_argument" />
+        <expand macro="c_and_o_argument">
+            <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
+        </expand>
         <expand macro="split" />
         <expand macro="print_header" />
         <conditional name="genome">
@@ -49,7 +51,7 @@
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
             <repeat name="c_and_o_argument_repeat">
-                <param name="cols" value="5" />
+                <param name="col" value="5" />
                 <param name="operation" value="mean" />
             </repeat>
             <output name="output" file="mapBed_result1.bed" ftype="bed" />
@@ -67,7 +69,7 @@
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
             <repeat name="c_and_o_argument_repeat">
-                <param name="cols" value="5" />
+                <param name="col" value="5" />
                 <param name="operation" value="collapse" />
             </repeat>
             <param name="strand" value="-S" />
@@ -77,7 +79,7 @@
             <param name="inputA" value="mapBed1.bed" ftype="bed" />
             <param name="inputB" value="mapBed2.bed" ftype="bed" />
             <repeat name="c_and_o_argument_repeat">
-                <param name="cols" value="5" />
+                <param name="col" value="5" />
                 <param name="operation" value="collapse" />
             </repeat>
             <param name="strand" value="-s" />
diff -r 457b09031d57 -r 2cd7e321d259 mergeBed.xml
--- a/mergeBed.xml	Tue May 19 07:05:36 2015 -0400
+++ b/mergeBed.xml	Wed May 27 12:54:35 2015 -0400
@@ -28,7 +28,9 @@
             label="Maximum distance between features allowed for features to be merged"
             help="That is, overlapping and/or book-ended features are merged. (-d)"/>
         <expand macro="print_header" />
-        <expand macro="c_and_o_argument" />
+        <expand macro="c_and_o_argument">
+            <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" />
+        </expand>
     </inputs>
     <outputs>
         <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/>
diff -r 457b09031d57 -r 2cd7e321d259 shuffleBed.xml
--- a/shuffleBed.xml	Tue May 19 07:05:36 2015 -0400
+++ b/shuffleBed.xml	Wed May 27 12:54:35 2015 -0400
@@ -42,6 +42,7 @@
                 <option value="not_be">Coordinates in which features from -i should not be placed?</option>
                 <option value="be">coordinates in which features from -i should be placed?</option>
             </param>
+            <when value="no" />
             <when value="not_be">
                 <param name="excl" type="data" format="bed" label="Choose File" />
                 <expand macro="overlap" />